Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/025ba8ad7284482ffa30e9aaea7f30/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BKVO-N1-BDNA-1_A23NLN3LT4_1/1029_BKVO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/025ba8ad7284482ffa30e9aaea7f30/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_BKVO-N1-BDNA-1_A23NLN3LT4_1/1029_BKVO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BKVO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_BKVO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BKVO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BKVO-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 67195954 total, 53380 skipped (flags/unmapped)
Fragments: 33694484 total (33408672 tlen-paired, 2855 hash-paired, 322 singletons, 15535 discordant, 267100 orphans, 10514 too large [>5000 bp], 11248339 duplicates)
Reads: 71644855 total, 42375 skipped (flags/unmapped)
Fragments: 35927485 total (35644050 tlen-paired, 1934 hash-paired, 354 singletons, 10529 discordant, 270618 orphans, 9241 too large [>5000 bp], 11845220 duplicates)
Reads: 79094922 total, 48360 skipped (flags/unmapped)
Fragments: 39666218 total (39330119 tlen-paired, 3854 hash-paired, 267 singletons, 15987 discordant, 315991 orphans, 15192 too large [>5000 bp], 13380730 duplicates)
Reads: 79526187 total, 75682 skipped (flags/unmapped)
Fragments: 39973120 total (39214061 tlen-paired, 1935 hash-paired, 336 singletons, 144263 discordant, 612525 orphans, 58563 too large [>5000 bp], 13459504 duplicates)